All players implicated in December's Mitchell Report on performance-enhancing drugs were given amnesty as part of the agreement, which toughens baseball's drug rules for the third time since the program began in 2002.
Thus, the deal eliminated 15-day suspensions assessed against Jose Guillen and Jay Gibbons.
The independent administrator, a position created in November 2005, will be given an initial three-year term and can be removed only if an arbitrator finds cause. Until now, he could be fired at any time by either side.
But baseball did not heed advice from the World Anti-Doping Agency and turn drug testing over to an outside agency.
In addition, the decision over whether a player can be subjected to reasonable-cause testing will remain with management and the union, with any disagreement decided by the sport's regular arbitrator. Also, a joint management-union body called the Treatment Board will supervise the part of the program relating to drugs of abuse, such as cocaine.
As part of the agreement, players will join Major League Baseball's efforts to educate youth about performance-enhancing drugs, and their union will contribute $200,000 to an anti-drug organization.
In exchange for those two provisions, baseball commissioner Bud Selig agreed not to discipline players implicated by Mitchell during his 1½-year investigation.
"We are gratified that commissioner Selig chose to accept Sen. Mitchell's recommendation that no further punishment of players is warranted," union head Donald Fehr said. "In many instances the naming of players was punishment enough; in others it may have been unfair."
Guillen and Gibbons were suspended in December following media reports linking them to performance-enhancing drugs. Those penalties were put on hold just before opening day as negotiators neared an agreement.
"It is time for the game to move forward," Selig said. "There is little to be gained at this point in debating dated misconduct and enduring numerous disciplinary proceedings."
The sides agreed that in future investigations, allegations against players won't be made public unless discipline is imposed, and that a player will be given the allegations and evidence against him before any investigatory interview.
While the sides agreed that records of negative tests be kept for two years, they did not agree to keep the actual urine samples.
Players and owners reached their first joint drug agreement in August 2002, then under pressure amended it in January 2005 and instituted a 10-day penalty for first offenses. After Congress pushed for more changes, they amended it a second time in November 2005, changing the first offense to a 50-game suspension, banning amphetamines and creating the independent program administrator, who shared power with a management-union Health Policy Advisory Committee.
According to a, many fans do not believe that the use of performance-enhancing substances dominates the game, but more suspect player involvement today than did a few years ago.
In his recommendations, Mitchell said the program should be administered "by a truly independent authority" in the form of an expert who couldn't be removed except for good cause, an independent nonprofit corporation or another structure created by the sides.
As a result, the HPAC is being disbanded, and its duties largely turned over to the administrator, Dr. Bryan Smith.
In the deal, the sides agreed:
The sides also disclosed a previously unannounced agreement struck during the 2006 labor talks in which they specified the commissioner has authority to discipline players under a just cause standard for violations of the drug agreement that don't carry a specified penalty.
"Going into this negotiation, the commissioner was 100 percent correct that we had the best program in professional sports," said Rob Manfred, baseball's executive vice president for labor relations. "These changes just solidify that kind of premier leadership position in my view."
The new joint drug agreement, which must be ratified by both sides, runs until Dec. 11, 2011, when baseball's labor contract expires. The sides will meet annually with the IPA, the collection company and the laboratory to consider changes.
"Given the series of modifications which have previously been made, as well as the flexibility provided for in the current JDA, we do not expect to be renegotiating the JDA again prior to the next scheduled round of collective bargaining," Fehr said.
Selig's next step will be to determine whether management employees should be disciplined for conduct mentioned in the Mitchell Report. He already has met with officials of the San Francisco Giants, who were mentioned prominently. Manfred said no decisions on management discipline have been made.
Selig said any fines imposed on management will be donated to the Partnership of a Drug Free America and the Taylor Hooton Foundation.